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#{\footnote {\fs16\up6 #} OVERVIEW}
${\footnote {\fs16\up6 $} Overview of Chemical Kinetics Simulator (CKS)}
K{\footnote {\fs16\up6 K} Overview}
+{\footnote {\fs16\up6 +} Help:005}
\plain\b\fs22 Overview of Chemical Kinetics Simulator (CKS)\plain \par
\par
\par
\plain \fs22 The Chemical Kinetics Simulator (CKS) provides a rapid, interactive 
method to simulate chemical reaction mechanisms. It lets you create detailed 
models of a wide range of reactions, without requiring additional programming.  
You can model homogeneous systems and also, using simple techniques, a variety 
of inhomogeneous systems. CKS uses a 
{\ul stochastic}{\v DEFINITION_STOCHASTIC}  method, based on 
reaction probabilities, to calculate the time history of a chemical system using 
the reaction's 
mechanism and the initial conditions you specify. It treats the reacting system 
as a volume filled with a limited number of 
{\ul particles}{\v DEFINITION_PARTICLE}  which represent reactants and products. \par
\par

\plain \b\fs22 Using Chemical Kinetics Simulator (CKS)\plain \fs22 \par
CKS makes it easy for you to input data and display results. Since the simulation engine can run 
as a background process within the program you can use CKS to set up simulations and examine 
data from previous calculations while running a simulation.\par
\par
CKS only requires basic information:  the reaction mechanism and kinetics, initial concentrations, 
reaction conditions, and several simulator setup parameters. You enter the reaction mechanism in 
conventional chemical notation, with complete flexibility in how you represent reaction species. You 
can select reaction conditions to be any physically realistic combination of constant, variable and 
programmed temperature, constant and variable volume, and constant and variable pressure. If 
reversible steps in the mechanism come into equilibrium, a situation which is often handled 
inefficiently by stochastic techniques, an equilibrium detection and emulation option lets you 
minimize the computer calculation time. CKS provides you with a notebook for each reaction file so 
you can keep written records as you develop and test a mechanism.\par
\par

\plain \b\fs22 Simulation results\plain \fs22 \par
Once a simulation is complete, you select the types of data plots to display. You can choose up to 
four plots of concentration, temperature, pressure and volume vs. time, and concentration, pressure 
and volume vs. temperature, depending on the run conditions. You may also import a data set to 
overlay onto the simulation results. You can print the plot window directly to an attached printer, 
prepare tables of data to be saved for further analysis, or save it in PostScript or Hewlett-Packard 
Graphics Language format for export to other applications, or direct high resolution output. A text 
summary of your reaction, including the mechanism, species data, simulator and reaction conditions, 
and your notebook text, can be prepared automatically; you can view or print it with any ordinary 
text editor. \par
\par
\par
\plain \b\fs22 Other Topics to help you get started:\plain \fs22 \par

\pard \fi720 \plain \fs22
{\uldb How to Run a Simulation : a quick tutorial}{\v TUTORIAL}\par
{\uldb Using the Main Window}{\v MAIN_WINDOW}\par
{\uldb Using the Main Menus}{\v MAIN_MENU}\par
{\uldb Conventions used in CKS Help}{\v CONVENTIONS}\par
\pard\page 

#{\footnote {\fs16\up6 #} MAIN_WINDOW}
${\footnote {\fs16\up6 $} Using the Main Window}
K{\footnote {\fs16\up6 K} Main Window;listbox;help line;}
+{\footnote {\fs16\up6 +} Help:015}
\b\fs22 Using the Main Window\plain \par
\par
\par
\plain \fs22 
All of CKS's functions are accessed through the main window. 
It contains information on the currently active reaction scheme, whose 
reaction steps are displayed in the 
{\ul reaction listbox}{\v DEFINITION_REACTION_LISTBOX} .  The 
reaction scheme and associated reacton conditions can be entered and modified using the main 
menu bar and 
{\ul pushbuttons}{\v DEFINITION_PUSHBUTTON} . The help line prompts the next action depending  
on what is currently highlighted.
\par
\par
\plain \b\fs22 Menu bar\plain \fs22 \par
When you click on a command from the main menu bar, another menu is displayed.  This 
{\ul pull-down menu}{\v DEFINITION_PULL_DOWN_MENU}  gives you access to another set of commands 
and windows.  The six pull-down menus which 
control CKS's functions are {\b File}, {\b Edit}, {\b View}, {\b Simulation}, {\b Results} 
and {\b Help}.
\par
\par
\plain \b\fs22 Current Reaction Scheme\plain \fs22 \par
This area tells you the name and sequence number of the current file, its processing status, the  
amount of computer time the most recent simulation took and the number of data points generated, 
the number of reaction steps, and the total number of reaction species.\par
\par
\plain \b\fs22 Reaction list\plain \fs22 \par
The reaction listbox displays all of the reaction steps defined for the current reaction scheme.  Click 
on a reaction step to highlight it.  Double-click on a step to open its Reaction Data Entry window.\par
\par
\plain \b\fs22 Pushbuttons\plain \fs22 \par
The pushbuttons at the bottom of the window affect the highlighted reaction step. 
{\b [Add Step...]} 
adds a blank line to the reaction list immediately below the highlighted one and the Reaction Data 
Entry window opens automatically.  {\b [Edit Step...]} opens the Reaction Data Entry window for this 
step.  {\b [Delete Step...]} deletes this step. \plain {\i This cannot be undone}. \par
\par
\plain \b\fs22 Help line\plain \fs22 \par
The help line, located at the bottom of the window, gives you more information about the part of the 
main window your cursor is currently resting on, or the menu item you have just clicked.\par
\par
\par
\plain \b\fs22 Other relevant topics:\plain \fs22 \par
\pard \fi720
{\uldb Using the Main Menus\plain}{\v MAIN_MENU}\par

\par \pard\page 


#{\footnote {\fs16\up6 #} MAIN_MENU}
${\footnote {\fs16\up6 $} Using the Main Menus}
K{\footnote {\fs16\up6 K} Main Menu}
+{\footnote {\fs16\up6 +} Help:020}
\plain \fs22 \plain \b\fs22  \plain \b Using the Main Menus\plain \fs22 \par
\par
\par
\plain \fs22 The File, Edit, Simulation, Results and Help menus let you access all of CKS's options and 
functions.\par
\par
The 
{\b File} menu allows you to create, save and retrieve reaction files which contain all of your data 
for a particular simulation.\par
\par
The {\b Edit} menu lets you enter and edit a reaction mechanism, reaction species data, and any 
explanatory notebook text.  It becomes active when a reaction scheme has been created or loaded 
from disk.\par
\par
The {\b Simulation} menu allows you to select the operating conditions for the CKS simulator, and to 
run the simulation.\par
\par
The {\b Results} menu displays the data from the simulation.  It is only available after a simulation of 
the current reaction scheme has been performed.  You may also view the results of a reaction that 
was run previously and saved, unless the reaction data are modified after the simulation.\par
\par
The {\b Help} menu gives you information on using CKS's help system, an overview of CKS, and the 
basic procedure for simulating a chemical reaction.\par
\par
\par
\par
\pard 
\plain \b\fs22  For more information, look at the following topics:\plain \fs22 \par
\pard \fi720\sl0
{\uldb Using the File Menu}{\v MENU_FILE}\par
{\uldb Using the Edit Menu}{\v MENU_EDIT}\par
{\uldb Using the View Menu}{\v MENU_VIEW}\par
{\uldb Using the Simulation Menu}{\v MENU_SIMULATION}\par
{\uldb Using the Results Menu}{\v MENU_RESULTS}\par
{\uldb Conventions Used in CKS Help}{\v CONVENTIONS}\par
\par \pard
\page 


#{\footnote {\fs16\up6 #}TUTORIAL}
${\footnote {\fs16\up6 $}How to Run a Simulation}
K{\footnote {\fs16\up6 K}simulation;tutorial}
+{\footnote {\fs16\up6 +}Help:010}
\b\fs22 How to Run a Simulation :  a quick tutorial \plain \fs22 \par
\pard 
\par
\par
\pard \sl0 
{\b 1. Open the Reaction File} \par
\par
Select {\b File|Create...}.  Two dialog windows will appear.  At the first, specify a name and location for the 
reaction scheme. The default location for the 
reaction files can be set by selecting {\b File|Preferences...}.  At the second window, select the time, 
energy, concentration and volume units to be used for data input and output.  {\i This is the only time 
the units can be specified for a file.} \par
\par
\par
{\b 2. Enter the Reaction Mechanism.} \par
\par
Click the {\b [Add Step...]} pushbutton at the main window.  The Reaction Data Entry window opens 
so that you may enter an individual reaction step in conventional chemical notation, along with its 
rate constants and rate law.  You can also open this window by selecting {\b Edit|Reaction 
Scheme...}.  More detailed help is available at this window.\par
\par

\par
{\b 3. Enter the Reaction Conditions.} \par
\par
Select {\b Edit|Reaction Conditions...}.  At this window, you enter initial concentrations for species 
present in the system. Use the radio buttons to choose the reaction condition options:  constant or 
variable temperature, pressure or volume, or programmed temperature.  More detailed help is 
available at this window. \par
\par

\par
{\b 4. Enter Species Data (for variable temperature and volume simulations).} \par
\par
Various physical data for species present in the reacting system are required if variable 
temperature and/or variable volume conditions are selected.  Select 
{\b Edit|Species Data...} to input 
data such as heats of formation, heat capacities and molar densities.  More detailed help is 
available at this window.  \par
\par
\par
{\b\ 5. Enter simulation parameters.} \par
\par

Select {\b Simulation|Simulation Settings...} .  The parameters you can set here include the number 
of {\ul particles}{\v DEFINITION_PARTICLE}  used to represent chemical species in the simulation, 
the number of {\ul events}{\v DEFINITION_EVENT} , the 
interval at which the status of the system is to be saved, an optional flag to stop the simulation at 
a particular time in the reaction, the 
{\ul random number seed}{\v DEFINITION_RANDOM_NUMBER_SEED}  for propagation of the simulation, and 
parameters specific to simulations of equilibria and variable temperature reactions.  More detailed  
help is available at this window.  \par
\par

\par
{\b 6. Run the Simulation.} \par
\par
Start the simulation by selecting {\b Simulation|Start}.  A window showing the status of the simulation 
will open.  While the simulation is in progress, you may not edit the currently active simulation file, 
but you can examine the results of a previous simulation or enter a new reaction scheme.\par
\par

\par
{\b 7. End the Simulation.} \par
\par

The simulation will stop when it has reached the "Total number of events" or the maximum 
simulation time defined in Step 5 above, or when all event probabilities are zero.  The simulation 
can be interrupted at any time without data loss by clicking the  
{\b Stop Simulation} pushbutton.  If 
you then look at the simulation results (Step 8) and decide to continue the simulation, restart the 
simulation by selecting {\b Simulation|Resume}. \par
\par

\par
{\b 8. Display the Simulation Results.} \par
\par

You can view the results of the simulation by selecting 
{\b Results|Plot Results...}.  This activates a 
dialog window that allows you to select among a variety of options for plotting the simulated data.  
After you choose the data, click the {\b [Plot]}  pushbutton to display the plot.  The plot window 
contains pushbuttons which additional menu options for display and export of data.  More detailed 
help is available at both the Simulation Results and the X/Y Plot window.  \par
\par

\par
\par \pard
\page 


\pard \sl0 
#{\footnote {\fs16\up6 #}MENU_FILE}
${\footnote {\fs16\up6 $}Using the File Menu}
K{\footnote {\fs16\up6 K}File Menu;slot;reaction file slot;}
+{\footnote {\fs16\up6 +}Help:025}
\plain \b\fs22  Using the File Menu\plain \fs22 \par
\par
The {\b File} menu allows you to create, save and retrieve reaction files which contain all of your data 
for a particular simulation.\par
\par
{\b Opening, saving and closing reaction files} \par
You begin working with CKS by opening or creating a reaction file: select either 
{\b Open...} or 
{\b Create...} from this menu.  The file will be placed in the next available reaction file 
{\ul slot}{\v DEFINITION_SLOT} . Once your 
file is open, and you begin to modify it, you can save your changes by selecting either 
{\b Save} or {\b\ Save As...}.  When you are ready to close the file, select 
{\b Close} .  When you select Open..., Create... or 
Save As..., a file selection window opens where you can specify the name and location of your 
reaction file.  Default application options for the 
{\ul file selection search templates}{\v DEFINITION_FILE_SEARCH_TEMPLATE}  can be set using the 
{\b Preferences} option.\par
\par
{\b Making a text summary of your reaction file} \par
CKS can create a text file in a standardized format which lists the reaction file name, each reaction 
step with its accompanying rate data, each reaction species and its initial concentration and species 
data, the reaction conditions, and the simulation conditions.  This file can be read with a 
conventional text editor or browser, and printed.  To make or update a text summary, select 
{\b Make Text Summary...}.  A file selection window opens.  When you have entered the filename and 
directory, click {\b [OK]}.  The file name and time of creation are noted at the top of the text file.\par
\par
\plain \b\fs22 Exiting CKS\plain \fs22 \par
To end your CKS session, select {\b Exit}. You will be asked whether you want to save any reaction 
schemes which have been modified since they were last saved.\par
\par
\par
\plain \b\fs22 Other related topics:\plain \fs22 \par
\pard \fi720\sl0
{\uldb Setting Application Options}{\v FILE_PREFERENCES}\par
{\uldb Creating Reaction Files}{\v FILE_CREATE} \par
{\uldb File Selection Windows}{\v FILE_SELECTION}\par
\pard \sl0 
\par
\par \pard
\page 
\pard \sl0 




#{\footnote {\fs16\up6 #}MENU_VIEW}
${\footnote {\fs16\up6 $}Using the View Menu}
K{\footnote {\fs16\up6 K}View Menu;slot;reaction file slot;}
+{\footnote {\fs16\up6 +}Help:028}
\plain \b\fs22  Using the View Menu\plain \fs22 \par
\par
The {\b View} menu allows you to display an open reaction file. A list of the nine reaction file 
{\ul slots}{\v DEFINITION_SLOT}, and the 
names of any files loaded in them, are displayed.  Select a reaction file by clicking on it.  The 
reaction file is displayed, and you may view and edit it.\par
\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}FILE_PREFERENCES}
${\footnote {\fs16\up6 $}Setting User Preferences}
K{\footnote {\fs16\up6 K}Preferences;Configuring CKS;Application Options;defaults;file search template}
+{\footnote {\fs16\up6 +}Help:050}
\plain \b\fs22 Setting Application Options\plain \fs22 \par
\par
\par
\plain \fs22 This dialog window lets you specify your preferences for CKS default options, including the file 
search template, window position and size, and over-write confirmation.  \par
\par
{\b Default File Templates} \par
The data entry fields are used to specify a 
{\ul file search template}{\v DEFINITION_FILE_SEARCH_TEMPLATE} .\par
\par
The REACTION FILE TEMPLATE is used for files containing reaction schemes.  They contain the 
data which describe the reaction scheme, and simulation results.  \par
 \par
The TEXT OUTPUT FILE TEMPLATE is used for output files containing data in text form, such as a 
summary of a reaction scheme, or a table of the simulation results.  \par
\par
The GRAPHICS OUTPUT FILE TEMPLATE applies to PostScript or HPGL output files created from 
X-Y plot data.  \par
\par
The EXTERNAL DATA FILE TEMPLATE applies to input files containing experimental or calculated 
data for comparison to simulation results.  The internal format of these files is described in the help 
screen for the Simulation Results window.\par
\par
The TEMPERATURE PROFILE TEMPLATE is used for input files containing time-temperature data 
used for programmed temperature calculations.  Their format is given in the help for the Select 
External Temperature Profile window.\par
\par
{\b Application options}\par
Two additional options can be selected using the checkboxes at the bottom of the window.  \par
\par
The WINDOW POSITION/SIZE can be changed for the Main and X/Y Plot windows using the mouse 
to drag the edges or top bar.  Check this option to save the positions and sizes of the windows 
between sessions.  \par
\par
Check the CONFIRM OVER-WRITE OF EXISTING FILE box to insure that a file is not inadvertently 
re-used.  If you attempt to write over an existing file,  a dialog box will ask you to confirm that it is 
OK to proceed.  \par
\par
\par
The following pushbuttons are available at the bottom of the window.  \par
\par
{\b [OK]} accepts the displayed values and closes the dialog window.  \par
\par
{\b [Undo]} resets the file templates and checkboxes to their values when the dialog window was 
opened.  \par
\par
{\b [Defaults]} resets all options to their default values.\par
\par
\par \pard
\page 


\pard \sl0 
#{\footnote {\fs16\up6 #}FILE_CREATE}
${\footnote {\fs16\up6 $}Creating reaction files}
K{\footnote {\fs16\up6 K}Create;creating;new}
\plain \fs22 \b Creating Reaction Files\plain \par
\par
\par
\plain \fs22 When you create a new reaction scheme, you specify its name, location and the units to be used for 
all data.\par
\par
The newly created reaction file will be placed in the first available 
{\ul slot}{\v DEFINITION_SLOT}.  If all slots are filled, CKS 
will ask you whether you wish to remove the currently active reaction scheme from memory.  If you 
wish to remove a different reaction scheme, you may use 
{\b File|Select} to select a different slot.\par
\par
{\b To create a new reaction scheme:} \par
1. Select {\b File|Create...}.   A file selection window opens.\par
2. Select the drive and directory where you wish to store your new file.\par
3. Enter the name of your new reaction file.\par
4. Click {\b [OK]}.  A units selection window opens.\par
5. Select units using the appropriate drop-down listbox.  Once chosen, they cannot be changed.\par
6. Click {\b [OK]}.  You return to the main window.\par
7. Select {\b File|Save} to save the new file to disk.\par
\par
From here, you may enter the reaction steps.\par
\par
\par
\plain \b\fs22 For more about creating new reaction files:\plain \fs22 \par
\pard \fi720\sl0
{\uldb Selecting Units for a New Reaction Scheme}{\v UNITS}\par
\par \pard
\page 


\pard \sl0 
#{\footnote {\fs16\up6 #}FILE_SELECTION}
${\footnote {\fs16\up6 $}File selection windows}
K{\footnote {\fs16\up6 K}file selection window;file search template;}
\fs22 \plain \b File selection windows\plain \par
\par
\par
\plain \fs22 These are used to specify a filename when you create or open a reaction file, external data file, text 
summary or plot file.  When the window is first opened, the file information given in your 
{\ul file search template}{\v DEFINITION_FILE_SEARCH_TEMPLATE}  is displayed.\par
\par
TO SELECT AN EXISTING FILE NAME :  Click the desired file name in the File Name listbox, then 
click {\b [Open]} .  You may also double-click on the desired file name.  \par
\par
TO SPECIFY A NEW FILE NAME :  Click in the File Name entry field and type the new file name. \par
\par
TO SELECT A DIFFERENT DRIVE:  Click on the {\b [Desktop]} pushbutton to select another drive on the desktop.\par
\par
TO SELECT A DIFFERENT DIRECTORY:  Select the pop-up menu displaying the name of the current 
directory and release the mouse button on the name of the desired higher-level 
directory. \par
\par
TO SPECIFY A DIFFERENT DEFAULT FILE SEARCH TEMPLATE :  You can change the file search template 
by selecting {\b File|Preferences...}. \par
\par
\par
The following additional pushbuttons are available for this dialog window:  \par
\par
{\b [Open]} or {\b [Save]} loads or saves the current selected file.\par
\par
{\b [Cancel]} closes this window without selecting a file.\par
\par
\par
\plain \b\fs22 Other relevant topics:\plain \fs22 \par
\pard \fi720\sl0
{\uldb Listboxes}{\v LISTBOXES}\par
\pard \sl0 
\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}UNITS}
${\footnote {\fs16\up6 $}Selecting Units for a New Reaction Scheme}
K{\footnote {\fs16\up6 K}Selecting Units; Creating a New Reaction Scheme}
+{\footnote {\fs16\up6 +}Help:055}
\plain \fs22 \b Selecting Units for a New Reaction Scheme\plain \fs22 \par
\par
\par
This dialog window allows UNITS for the simulation to be selected.  
{\i This is the only time this window 
will appear for this particular reaction scheme!}  \par
\plain \fs22 \par
Four unit groups are listed in the window:  CONCENTRATION, TIME, PRESSURE and ENERGY.  
Unit types from each group can be selected in any combination by selecting options from the drop-
down listboxes.\par
\par
The units chosen must be used consistently for all input data (reminders for the active units are 
listed on the data entry dialog windows as needed), and will be used for plotting the simulation 
results.  \par
\par
\par
The following pushbuttons are available at the bottom of the window.  \par
\par
{\b [OK]} accepts the selected units and returns you to the main window.  \par
\par
{\b [Defaults]} selects default options in all four listboxes.  \par
\par
\par
\par
{\b Other relevant topics:} \par
\pard \fi720\sl0
{\uldb Listboxes}{\v LISTBOXES} \par
{\uldb Creating Reaction Files}{\v FILE_CREATE} \par
\pard \sl0 
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}LISTBOXES}
${\footnote {\fs16\up6 $}Listboxes}
K{\footnote {\fs16\up6 K}listbox;listboxes}
\plain \fs22 \b Listboxes\plain \par
\par
\par
\plain \fs22 Listboxes allow you to select individual items for data entry or plotting.  They come in three types:\par
\par
o DROP-DOWN LISTBOX.  The current selection is displayed in the window.  To view available 
options, click on the adjacent button or the display window.  To select a listed item, click on it.  This 
type of listbox is used for units and font size selection.\par
\par
o SINGLE SELECTION LISTBOX.  The current selection is highlighted in a window which displays a 
list of all choices.  Click on an item to select it.  This type of listbox is used for species 
concentrations and the reaction list.  When you double-click on a reaction step in the main window 
listbox, the Reaction Data Entry window for that step opens.\par
\par
o MULTIPLE SELECTION LISTBOX.  One or more currently selected items is highlighted in a 
window which displays a list of all choices.  To select or de-select a single item, click on it.  
To select multiple items, press and hold the Command key while clicking the items. This type of 
listbox is used to select species to plot.\par
\par
\par \pard\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}MENU_EDIT}
${\footnote {\fs16\up6 $}Using the Edit Menu}
K{\footnote {\fs16\up6 K}Edit Menu;reaction scheme;cut;copy;paste;editing reaction steps}
+{\footnote {\fs16\up6 +} Help:030}
\plain \fs22 \b Using the Edit Menu\plain \fs22 \par
\par
\par
This menu lets you edit the reaction mechanism and species data, and explanatory notebook text.  It 
is only active after a reaction scheme has been created or loaded from disk.\par
\par
{\b The Reaction Scheme} \par
After you have created a new reaction scheme, or loaded an existing one into memory, the reaction 
mechanism appears in the listbox on the CKS main window.  You can now enter the reaction step, 
rate constants and rate law; the initial concentration and pressure, temperature and volume 
conditions; species data, if variable temperature and/or variable volume conditions have been 
selected; and explanatory notebook text.  Select 
{\b Reaction Scheme...}, {\b Reaction Conditions...},
{\b Species Data...} and {\b Notebook....}, respectively, to enter this information.\par
\par
{\b Editing a reaction scheme at the main window} \par
You may cut or copy a reaction step displayed in the main window listbox and paste it in another 
location in your current reaction scheme, or into any reaction scheme loaded in CKS's memory.  
This can save you substantial amounts of time as you create and edit reaction files.  The reaction 
step, rate constants and rate law are transferred in this process.  
{\i Any other information, i.e. species 
concentrations and data, must be entered separately.} \par
\par
{\b Example:  moving a reaction step to another scheme} \par
1. Highlight the reaction step you wish to cut or copy.\par
2. Select {\b Cut} or {\b Copy}.  The reaction step is placed on the CKS clipboard.\par
3. Display the reaction file in which you will paste the reaction step by selecting its name using 
{\b File|Select} .\par
4. Highlight the step under which the step is to be placed.\par
5. Select {\b Paste}.\par
\par
\par
\plain \b\fs22 Related topics:\plain \fs22\par
\pard \fi720\sl0
{\uldb The Reaction Scheme}{\v REACTION_DATA_ENTRY}\par
{\uldb Reaction Conditions}{\v REACTION_CONDITIONS}\par
{\uldb Entering and Editing Species Data}{\v SPECIES_DATA}\par
{\uldb Using the Notebook}{\v NOTEBOOK}\par
\pard \sl0 
\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}REACTION_DATA_ENTRY}
${\footnote {\fs16\up6 $}The Reaction Scheme}
K{\footnote {\fs16\up6 K}Reaction Data Entry;reaction step;rate law;rate constant}
\plain \fs22 \b The Reaction Scheme\plain \par
\par
\par
\plain \fs22 You enter and edit your reaction scheme at the Reaction Data Entry window.  You type in the 
reaction step, specify the type of rate constant, enter the rate constant(s), and specify the rate law.  
You must fill in all sections of this window before you may enter a new reaction step.\par
\par
You may display sequentially data for each reaction step by using the up- and down-arrow 
pushbuttons in the upper left corner of the window.\par
\par
{\b [OK]} stores the information at this screen in memory, and returns you to the main window.\par
\par
{\b [Add Another]} stores the information in memory, adds another reaction step after this one, and 
displays the blank Reaction Data Entry window for that step.\par
\par
{\b [Delete This]} deletes this reaction step and the accompanying data at this window.\par
\par
{\b [Undo]} restores the last saved values for this reaction step.\par
\par
\par
{\b Related topics:} \par
\pard \fi720\sl0
{\uldb The Reaction Step}{\v REACTION_STEP} \par
{\uldb Rate Constants}{\v RATE_CONSTANTS}\par
{\uldb Rate Law}{\v RATE_LAW}\par
{\uldb Editing a Rate Law}{\v RATE_LAW_EDIT}\par
\pard \sl0 
\par
\par \pard
\page 


\pard \sl0 
#{\footnote {\fs16\up6 #}REACTION_CONDITIONS}
${\footnote {\fs16\up6 $}Reaction Conditions }
K{\footnote {\fs16\up6 K}Reaction Conditions }
+{\footnote {\fs16\up6 +}Help:100}
\plain \fs22 \b Reaction Conditions\plain \fs22 \par
\par
\par
When CKS starts a simulation, it sets up internal information required for tracking temperature (T), 
volume (V) and pressure (P), and apportions 
{\ul particles}{\v DEFINITION_PARTICLE}  in the simulation volume according to the 
initial concentration(s) of the species present.  The Reaction Conditions window allows you to supply 
the concentration data and select among the available T, V and P options.\par
\par
{\b Initial reactant concentrations (amounts)} \par
{\b Initial reactant amounts} \par
To enter or review the initial concentrations (amounts), select the species to have initial non-zero 
concentrations by clicking on them in the Species Name listbox.  Enter the values in the "Initial 
concentration of..." data entry field.  If variable volume conditions are selected, you enter amounts, 
and concentrations are calculated from them internally.  The units are those specified when the 
reaction file was first created.  Floating point or scientific notation formats may be used, exponents 
may range from -308 to 308.  \par
\par
{\b System state} \par
Three groups of radio buttons allow combinations of PRESSURE, TEMPERATURE and VOLUME 
options to be chosen for the simulation.  Volume may be constant, variable, or not tracked; pressure 
may be constant or variable; and temperature may be constant or variable, or follow either a linear 
program or external profile.\par
\par
Not all combinations of them are allowed (or physically meaningful!).  The following list summarizes 
the available options.\par
\par

\f5 \pard \fi180
\b\fs22
  {\ul Pressure      Volume      Temperature} \par \par
  constant     variable       variable \par
  variable     constant       variable \par
  constant    not tracked     variable \par
  variable     constant      programmed \par
  constant     variable      programmed \par
  constant    not tracked    programmed \par
  constant    not tracked     constant \par
  variable     constant       constant \par
  constant     variable       constant \par
\par \pard \plain


{\b \fs22 For more about reaction conditions:} \par
\pard \fi720\sl0 \fs22
{\uldb Volume Options}{\v VOLUME} \par
{\uldb Temperature Options}{\v TEMPERATURE} \par
{\uldb Pressure Options}{\v PRESSURE} \par
\pard \sl0 
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}SPECIES_DATA}
${\footnote {\fs16\up6 $}Entering and Editing Species Data}
K{\footnote {\fs16\up6 K}Species Data;Physical State;Thermochemical Coefficients;variable temperature;variable volume;enthalpy;heat capacity;}
+{\footnote {\fs16\up6 +}Help:095}
\plain \b\fs22 Entering and Editing Species Data\plain \par
\par
\par
\plain \fs22 When variable volume and/or variable temperature conditions are selected, you must supply CKS 
with physical state and density information, and thermochemical coefficients as needed.  These data 
are entered at the Set Species Data window. Depending upon the reaction conditions you select, 
part or all of the data entry fields will be active.  Known or estimated data must be supplied for all 
species in the reaction system.  If you are not using variable volume and/or temperature reaction 
conditions, this window is not accessible.\par
\par
{\b Variable temperature simulations} \par
If temperature is variable then thermochemical coefficients must be specified for every species in the 
system.  Temperature changes are calculated from the change in the temperature dependent 
enthalpy of the system as the reaction proceeds and concentrations of various species increase and 
decrease.  The expression is:\par
\par
\pard \qc\sl0 
\plain \fs24{\i d} Hf(T) = {\i d} H0 + a + bT + cT^2 + dT^3 \par
\par
\pard \sl0 
\plain \fs22
where {\i d} H0 is the enthalpy in (kjoules or kcal)/mol and a, b, c and d are coefficients for the 
temperature dependent heat capacity in (joules or cal)/mol deg^n, n = 0 to 3. In precise calculations 
{\i d} H0 must be the enthalpy of formation at 0 K. If constant heat capacity is used, b = Cp and 
coefficients a, c and d are explicitly set equal to zero.  The coefficient b cannot be set to zero. \par
\par
{\b Variable volume simulations} \par
If volume is variable then both the Physical State and the molar density (in moles/unit volume) must 
also be specified for each species in order for the system volume to be calculated during the 
simulation.  Although a mixture of phases is allowed to be generated during a simulation, only one 
phase may be present initially, and only the volume of that phase is tracked.  \par
\par
To set or modify thermochemical or density values for a species, click on it in the "Species Name" 
listbox.  Then click on the value to be changed and type the new value in floating point or scientific 
notation formats. The allowed range of exponents is -308 to 308. To select a physical state for a 
species, click on the radio button corresponding to the desired state.\par
\par
\par
The following pushbuttons are available:  \par
\par
{\b [OK]} saves the current values of all parameters, and closes the dialog panel.  \par
\par
{\b [Undo]} resets all parameters for the currently selected species to their values when that species 
was selected in the "Species Name" listbox.  \par
\par
{\b [Defaults]} resets all parameters for the currently selected species to their default values.\par
\par
\par
{\b Other relevant topics:} \par
\pard \fi720\sl0
{\uldb Volume Options}{\v VOLUME}\par
{\uldb Temperature Options}{\v TEMPERATURE}\par
\pard \sl0 
\par
\par \pard
\page 


\pard \sl0 
#{\footnote {\fs16\up6 #}NOTEBOOK}
${\footnote {\fs16\up6 $}Using the Notebook}
K{\footnote {\fs16\up6 K}Notebook}
+{\footnote {\fs16\up6 +}Help:045}
\plain \fs22 \b Using the Notebook\plain \par
\par
\par
\plain \fs22 The notebook window lets you record information about the reaction scheme (for example, the 
purpose of a simulation, or comments on the reaction scheme or reaction conditions).  The text 
entered here is saved whenever the reaction file is saved. You may keep the window open as you 
build the reaction scheme or examine the simulation results, so that notes can be made as 
necessary.  If another reaction scheme in memory is made active (using {\b File|Select}) while the 
notebook window is open, the Notebook Entry window is hidden (but not closed) until the original 
reaction scheme is again made active.  \par
\par
To enter text, click on the text entry window and type.  The notebook can contain a maximum of 
5000 characters.  \par
\par
\par
The following pushbuttons are available in the notebook window:  \par
\par
{\b [OK]} accepts the current text in the notebook, and closes the window.  \par
\par
{\b [Clear]} erases all text from the notebook.  
{\i Beware!}  Text can only be restored using {\b [Undo]} if it 
has been previously saved by closing the notebook window.  \par
\par
{\b [Undo]} resets the notebook text to its state when the dialog window was most recently opened.  \par
\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}REACTION_STEP}
${\footnote {\fs16\up6 $}The Reaction Step}
K{\footnote {\fs16\up6 K}reaction step format;species mnemonics;mnemonic;reaction step;maximum number of reaction steps;}
\plain \fs22 \b The Reaction Step\plain \par
\par
\par
\plain \fs22 Individual reaction steps are entered at the Reaction Data Entry window much as they would be 
written on paper.  The generalized format for a non-reversible reaction is:\par
\par
\pard \qc\sl0 \fs24
x A + y B + z C => w D + v E\par
\par
\pard \sl0 \fs22
where x, y, z, w and v are stoichiometric coefficients in integer format, and A, B, C, D and E are 
mnemonics that you choose for the various reactants and products.  The format for a reversible 
reaction is:\par
\par
\pard \qc\sl0 \fs24
x A + y B + z C <=> w D + v E\par
\par
\pard \sl0 \fs22
Coefficients must be separated from species mnemonics by a blank space.  Arrows are typed as 
"equals" "greater than"  ( => ) or "less than" "equals" "greater than" ( <=> ).\par
\par
A mnemonic may be up to eight characters.  The first character must be alphabetic, and the others 
may be any letter, symbol or number excluding "<", ">", "+" and "=".  Mnemonics must be used 
consistently.  Up to four reactant and four product mnemonics may be used in each reaction step.   
Species may be given any name convenient to you.  They can correspond to real molecules, or to 
{\ul pseudo-species}{\v DEFINITION_PSEUDO_SPECIES} .\par
\par
The size of the simulation is limited by the memory available in the computer and the operating 
system you are using. The maximum number of reaction steps available on the Macintosh is 65,536. The 
order in which steps are entered is immaterial to the simulation.\par
\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}RATE_CONSTANTS}
${\footnote {\fs16\up6 $}Rate Constants}
K{\footnote {\fs16\up6 K}Reaction Data;Rate Constants}
+{\footnote {\fs16\up6 +}Help:120}
\plain \fs22 \b Rate Constants\plain \par
\par
\par
\plain \fs22 The rate constant can be entered either in temperature-dependent (Arrhenius) form, 
or as a temperature-independent, single valued constant.  Select the form of the rate constant by clicking on the 
appropriate radio button.  \par
\par
The general temperature-dependent form is \par
\par
\pard \qc\sl0 \fs24
k = A T^n exp (-E/RT) \par
\par
\pard \sl0 \fs22
where A is the pre-exponential A Factor, n is the Temperature Exponent, and E is the Activation 
Energy.  \par
\par
If the reaction is forward only, one set of parameters is entered.  If it is reversible, two sets are 
entered. Values may be in floating point or scientific notation formats, with exponents in the range 
-308 to 308.\par
\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}RATE_LAW}
${\footnote {\fs16\up6 $}Rate Law}
K{\footnote {\fs16\up6 K}rate law}
\plain \fs22 \b Rate Law \plain \fs22 \par
\par
\par
You have two options for specifying the rate law of the reaction step.  Usually it corresponds to the 
reaction step as written, and is derived by the simulator from the stoichiometry of the reaction step.  
Under some circumstances it can differ from the stoichiometry, however, and the "Define Special 
Rate Law" radio button allows the rate law to be EDITED.  When you select this button, the 
{\b [Edit Rate Law...]} pushbutton is activated and the Edit Special Rate Law window opens.  The Special 
Rate Law window can be opened at a later time by clicking on the pushbutton.  Detailed help for 
use of the Special Rate Law option is available at the window.\par
\par
\par
{\b Other relevant topics:} \par
\pard \fi720\sl0
{\uldb Editing a Rate Law}{\v RATE_LAW_EDIT} \par
\pard \sl0 
\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}RATE_LAW_EDIT}
${\footnote {\fs16\up6 $}Editing a Rate Law}
K{\footnote {\fs16\up6 K}Rate Law;special rate law}
+{\footnote {\fs16\up6 +}Help:125}
\plain \fs22 \b Editing a Rate Law\plain \par
\par
\par
\plain \fs22 The general form of a rate law R for a reaction step \par
\par
\pard \qc\sl0 \fs24
n A + m B + ... => products \par
\par
\pard \sl0 \fs22 
is \par
\par
\pard \qc\sl0 \fs24 
R = k [A]^n [B]^m...  \par
\par
\pard \sl0 \fs22 
where k is the rate constant, multiplied by reactant concentrations raised to an order equal to the 
stoichiometry in the reaction step.  For cases where the rate law should not be directly derived from 
the stoichiometry, it is specified separately using this dialog window.  \par
\par
As a starting point, CKS displays a sample rate law derived from the reactants in the step, allowing 
the user to change the exponents to the values required.  If the rate is independent of one or more 
of the reactants, enter a coefficient of 0 for the reactant(s).  If the rate law is known to depend on 
species which are not part of the stoichiometry, then the step should be rewritten to include those 
species as both reactants and products; in this manner, there is no net consumption of them but 
they appear in the sample rate law.  \par
\par
\par
The following pushbuttons are available:  \par
\par
{\b [OK]} stores the new rate law and returns to the Reaction Data Entry window.  \par
\par
{\b [Undo]} restores the exponents to their original values.  \par
\par
{\b [Default]} sets the values of all the exponents equal to the stoichiometric coefficients of the reactants 
in the current reaction step.\par
\par
\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}VOLUME}
${\footnote {\fs16\up6 $}Volume Options}
K{\footnote {\fs16\up6 K}volume}
\plain \fs22 \b Volume options\plain \fs22 \par
\par
The volume options can be used for all phases of matter.  \par
\par
{\b Constant volume} \par
The volume of the reacting system is held constant even though moles of species, temperature and 
pressure may change.  \par
\par
{\b Variable volume} \par
The volume of the reacting system is allowed to change as the number of moles of each species 
changes.  To use this option the densities and phases (gas, solid or liquid) of all species in the 
reaction must be specified by selecting {\b Edit|Species Data...} .\par
\par
The reacting system must start as a single pure phase, gas, liquid or solid, but can evolve to include 
more than one phase.  {\i Only the total volume of those species designated as having the initial phase 
is calculated.}  The volume of material in that phase is updated and used to renormalize the 
concentrations of all species after each event in the simulation.  Since the volume is only that of the 
initial phase, concentrations of species formed in new phases during the course of a reaction (e.g. 
gas evolved as a solid reacts) will not be correct.  No steps involving reactants in the new phases 
should be used in the reaction scheme, or the timebase of the simulation will {\i not} be meaningful. 
The simulator does not check for this.  \par
\par
{\b Volume not tracked} \par
The volume of the system is not explicitly calculated or constrained during the simulation.  This 
option saves computational overhead if variations in volume are expected to be small or are not of 
interest.  This option is mainly intended for condensed phase simulations.\par
\par
\par
{\b Other relevant topics:} \par
\pard \fi720\sl0
{\uldb Entering and Editing Species Data}{\v SPECIES_DATA}\par
\pard \sl0 
\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}TEMPERATURE}
${\footnote {\fs16\up6 $}Temperature Options}
K{\footnote {\fs16\up6 K}temperature;variable temperature;programmed temperature;temperature convergence standard;}
\plain \fs22 \b Temperature Options\plain \par
\par
\par
\plain \fs22 The reaction can run under isothermal or effective isothermal conditions, with the instantaneous 
temperature held constant or varied externally, or under adiabatic conditions, with the instantaneous 
temperature determined by the reaction enthalpy and the heat capacity of the species in the system.\par
 \par
{\b Constant temperature} \par
The reacting system is assumed to be isothermal, i.e.  the temperature is unchanged throughout the 
reaction. If Arrhenius parameters are used for one or more of the rate constants, the system 
temperature must be specified, otherwise no value need be given. The system temperature must be 
greater than 0 (zero) K. \par
\par
{\b Variable temperature} \par
The system is assumed to be completely insulated from its surroundings, and its temperature 
changes as the simulation proceeds because of heat released or taken up during the reaction. A 
non-zero  initial temperature must be specified.\par
\par
{\b Follow linear program} \par
The time-dependence of the temperature of the system is predetermined, and supplied to the 
simulator in the form of an analytic function.  \par
\par
{\b Follow external profile} \par
The time-dependence of the temperature of the system is predetermined, and supplied to the 
simulator as a table of time-temperature pairs which have been saved in a text file.   \par
\par
\par
Click the {\b [Change Settings...]} pushbutton to enter the data required for the temperature option you 
select. Additional help is available at the dialog window. \par
\par
 \par
{\b Other relevant topics:} \par
\par
\pard \fi720\sl0
{\uldb Entering and Editing Species Data}{\v SPECIES_DATA}\par
{\uldb Constant Temperature}{\v TEMPERATURE_CONSTANT} \par
{\uldb Variable Temperature}{\v TEMPERATURE_VARIABLE} \par
{\uldb Setting up a Linear Temperature Program}{\v TEMPERATURE_LINEAR} \par
{\uldb Programmed Temperature - Select External Profile}{\v TEMPERATURE_EXTPROF_EDIT} \par
\pard \sl0 
\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}TEMPERATURE_CONSTANT}
${\footnote {\fs16\up6 $}Constant Temperature}
K{\footnote {\fs16\up6 K}constant temperature;Arrhenius;}
\plain \fs22 \b Constant Temperature \plain \fs22 \par
\par
If Arrhenius parameters are used for any of the rate constants, the system temperature must be 
entered in the Reaction temperature data entry field. The value must be greater than 0 (zero) K.\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}TEMPERATURE_VARIABLE}
${\footnote {\fs16\up6 $}Variable Temperature}
K{\footnote {\fs16\up6 K}variable temperature;temperature convergence standard;}
\plain \fs22 \b Variable Temperature\plain \fs22 \par
\par
The initial temperature is typed in the Reaction temperature data entry field. It must be greater than 
0 (zero) K. Since CKS updates the system temperature after each 
{\ul event}{\v DEFINITION_EVENT}  in the simulation using an 
iterative procedure, you must also specify a 
{\ul temperature convergence standard}{\v DEFINITION_TEMP_CONV_STAND}.  Calculation of the 
new system temperature from the thermochemistry is iterative, and this parameter adjusts how finely 
or coarsely the new value is calculated.  A value of 0.5 degrees is satisfactory for most cases.  If 
there is any doubt, test the invariance of the result to halving the number.  The default value is 
somewhat smaller.\par
\par
\par
You also need to supply heat capacities and enthalpies for all species in the reaction.  They are 
entered by selecting {\b Edit|Species Data...} .  \par
\par
\par
{\b For more information:} \par
\par
\pard \fi720\sl0
{\uldb Entering and Editing Species Data}{\v SPECIES_DATA} \par
\plain \fs22 \par
\pard \sl0 
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}TEMPERATURE_LINEAR}
${\footnote {\fs16\up6 $}Setting up a Linear Temperature Program}
K{\footnote {\fs16\up6 K}Temperature Programming;linear program;programmed temperature}
+{\footnote {\fs16\up6 +}Help:130}

\plain \fs22 \b Setting up a Linear Temperature Program\plain \par
\par
\par
\plain \fs22 Here you can set up a temperature program of the form\par
\par
\pard \qc\sl0 \fs24
T(t) = T0 + bt\par
\par
\pard \sl0 \fs22
where T(t) is the time-dependent temperature, T0 is the initial temperature, b is the slope, and t is 
time.\par
\par
{\b Coefficients} \par
The INITIAL TEMPERATURE is specified in the first data entry field. It must be greater than 0 (zero) 
K.  The SLOPE is entered in the second field.  The slope can be positive or negative.\par
\par
{\b Maximum step size} \par
The maximum step size limits the temperature jump which the simulator can take as it progresses 
through the temperature program.  The size of an individual temperature step is determined by the 
{\ul time step}{\v DEFINITION_TIME_STEP}  size calculated for each 
{\ul event}{\v DEFINITION_EVENT} .
Since the time steps are calculated from the 
system's total 
reaction probability, when reactions are slow the steps can become too large for simulation accuracy 
to be maintained.  This happens frequently in  programmed temperature reactions. The maximum 
temperature step size is used to determine whether the simulation is proceeding smoothly; if the 
step size is exceeded special algorithms are used to control the simulation.  Typically a step size of 
10 K is adequate.  \par
\par
{\b Final temperature} \par
The final temperature is the upper or lower limit of the temperature program, depending on whether 
the slope is positive or negative. {\i When the limit is reached, the simulation is terminated.} \par
\par
{\b Note!} \par
The equilibrium detect option can be selected in combination with programmed temperature 
simulations using {\b Simulation|Settings...}, but it will not be active.\par
\par
\par
The following pushbuttons are available:  \par
\par
{\b [OK]} accepts the current values of the coefficients and closes the dialog panel.  \par
\par
{\b [Undo]} resets the coefficients displayed in the entry fields to their values when the dialog panel was 
activated.  \par
\par
{\b [Defaults]} resets the coefficients displayed in the entry fields to the default values.\par
\par
\par
{\b Other relevant topics:} \par
\pard \fi720\sl0
{\uldb Equilibrium Detect}{\v EQUILIBRIUM_DETECT} \par
\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}TEMPERATURE_EXTPROF_EDIT}
${\footnote {\fs16\up6 $}Programmed Temperature - Select External Profile}
K{\footnote {\fs16\up6 K}external temperature profile;programmed temperature;profile;}
\plain \fs22 \b Programmed Temperature - Select External Profile\plain \par
\par
\par
\plain \fs22 You may either select an existing 
{\ul temperature profile}{\v DEFINITION_TEMP_PROFILE}  file, or create your own. When the window is 
opened, the most recently selected profile is displayed.\par
\par
{\b Selecting a profile} \par
To select a profile from a profile library you may have on disk, click {\b [Select a File ...]}.  
This opens a 
file selection window where you can specify the name of the temperature profile you wish to use for 
your simulation.\par
\par
{\b Creating or changing a profile} \par
You may also use this window to enter or modify a profile while viewing it.  To create a new file, 
click {\b [Create New...]} .  To enter or edit data, click in the "Time Temperature" data entry field. The 
format of the file is pairs of points in the order:\par
\par
\pard \sl0 
time    temperature \par \par
The time points must be in order of increasing numerical value, and the first time point must be 0 
(zero). All temperature points must be greater than 0 K.  Data can be entered in floating point or 
scientific notation, with exponents ranging from -308 to 308.  If you wish to label the data columns, 
or include other non-numerical text, begin the line with an asterisk (*).  That line will not be read, but 
will be saved with the profile.  This lets you format the profile for importing into your data plots for 
comparison to simulation results. \par
\par
The maximum length of a profile is 32,768 characters. The primary restriction on the dynamic range 
of time and temperature values you may use in a profile is the precision allowed by the Macintosh.  As a 
guideline, keep your range within twelve orders of magnitude.\par
\par
{\b Displaying a profile} \par
To plot a profile as you enter data, click {\b [Refresh Plot]}.  It will be displayed using the color scheme 
specified at the X/Y Plot window.\par
\par
{\b Maximum step size} \par
The MAXIMUM STEP SIZE limits the temperature jump which the simulator can take as it 
progresses through the temperature program.  The size of an individual temperature step is 
determined by the 
{\ul time step}{\v DEFINITION_TIME_STEP}  size calculated for each 
{\ul event}{\v DEFINITION_EVENT} .  Since the time steps are calculated 
from the system's total reaction probability, when reactions are slow the steps can become too large 
for simulation accuracy to be maintained.  This happens frequently in  programmed temperature 
reactions. The maximum step size is used to determine whether the simulation is proceeding 
smoothly; if the step size is exceeded special algorithms are used to control the simulation.  
Typically a step size of 10 K is adequate.  \par
\par
{\b Note!} \par
If and when the final temperature in the profile is reached, the calculation is converted to a 
{\i constant temperature}  simulation at the final value.  It continues to run until the event limit is reached, or the 
total reaction probability has dropped to zero, or the maximum simulation time has been exceeded. \par
 \par
The equilibrium detect option can be selected in combination with programmed temperature 
simulations using {\b Simulation|Settings...}, but it will be inactive as long as the temperature in the 
simulation is determined by the profile. If the simulation converts to a constant temperature 
simulation at the end of a profile, the equilibrium detect and emulation option becomes active. \par
\par
The following pushbuttons are available:\par
\par
{\b [OK]} saves your profile to disk and returns you to the Reaction Data Entry window.\par
\par
{\b [Undo]} restores the values from your last saved version.\par
\par
{\b [Save As...]} lets you save the displayed time/temperature profile as a new file.\par
\par
\par
{\b Other relevant topics:} \par
\pard \fi720\sl0
{\uldb External data format}{\v EXTERNAL_DATA} \par
{\uldb Equilibrium Detect}{\v EQUILIBRIUM_DETECT}\par
\plain \fs22 \par
\pard \sl0 
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}PRESSURE}
${\footnote {\fs16\up6 $}Pressure Options}
K{\footnote {\fs16\up6 K}pressure;constant pressure;variable pressure;}
\plain \fs22 \b Pressure Options\plain \fs22 \par
\par
{\b Constant pressure} \par
This option maintains constant pressure in gas phase reactions.  It should also be selected for all 
condensed phase simulations.\par
\par
{\b Variable pressure} \par
Selection of this option allows the pressure in gaseous systems to be tracked as temperature and 
moles of species vary during a reaction.\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}VERIFY_SPECDATA}
${\footnote {\fs16\up6 $}Verifying Species Data}
K{\footnote {\fs16\up6 K}Species Data;verify;}
+{\footnote {\fs16\up6 +}Help:135}
\plain \fs22 \b  Verifying Species Data\plain \par
\par
\par
\plain \fs22 While preparing for the simulation, CKS has detected that you have made changes to the reaction 
scheme since the last time a simulation was initialized from it. This can include modification of a 
reaction step, addition of new steps, or changes in species mnemonics.  Please verify data for all 
species to be sure that the simulation will be performed as desired.  \par
\par
This dialog window displays the entire internal data set for each SPECIES in the reaction.  The 
currently active species is named in the top right corner of the window.  To select a new species 
click on its name in the Defined Species List box.  \par
\par
To enter an INITIAL CONCENTRATION, type the required value in the Initial concentration data 
entry field.  The units are those specified when the reaction file was first created.  Exponents may 
range from -308 to 308 if scientific notation is used.  \par
\par
If TEMPERATURE is variable then Thermochemical Coefficients must be specified for every species 
in the system.\par
\par
If VOLUME is variable then both the Physical State and the Molar Density (in moles/unit volume) 
must be specified for each species.\par
\par
\par
The following pushbuttons are available at the bottom of the window.  \par
\par
{\b [Start Simuln]} starts the simulation once the data have been verified.  \par
\par
{\b [Cancel Simuln]} returns to the main CKS window without performing a simulation.  \par
\par
{\b [Default Values]} resets all data fields to their default values.  \par
\par
{\b [Undo Changes]} restores all data fields to their values when the window was opened.  \par
\par
\par
{\b Other relevant topics:} \par
\pard \fi720\sl0
{\uldb Volume Options}{\v VOLUME} \par
{\uldb Temperature Options}{\v TEMPERATURE} \par
{\uldb Entering and Editing Species Data}{\v SPECIES_DATA} \par
\pard \sl0 
\par
\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}VERIFY_SPECCONC}
${\footnote {\fs16\up6 $}Setting Species Concentrations}
K{\footnote {\fs16\up6 K}Concentrations;SIMULATION}
+{\footnote {\fs16\up6 +}Help:075}
\plain \fs22 \b Setting Species Concentrations\plain \par
\par
\par
\plain \fs22 Concentrations for all species are set to zero, and the simulation cannot run.  \par
\par
To enter initial concentrations for one or more species, select the species by clicking on it in the 
Species Name list box, and enter the required value in the "Initial concentration of..." data entry field.  
The units are those specified when the reaction file was first created. Values may be entered in 
floating point or scientific notation formats, with exponents in the range -308 to 308.  \par
\par
\par
The following pushbuttons are available:  \par
\par
{\b [Start Simuln]} starts the simulation after initial concentration(s) have been entered.  \par
\par
{\b [Cancel Simuln]} returns to the main CKS window without performing a simulation.  \par
\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}MENU_SIMULATION}
${\footnote {\fs16\up6 $}Using the Simulation Menu}
K{\footnote {\fs16\up6 K}Simulation Menu;Simulation Options;Starting a Simulation;stopping a simulation}
+{\footnote {\fs16\up6 +}Help:035}
\plain \fs22 \b Using the Simulation Menu\plain \fs22 \par
\par
\par
{\b Setting up the simulation} \par
Before you run a simulation, you may verify or change CKS's simulation parameters.  To do this, 
select {\b Simulation settings...} .\par
\par
{\b Starting and stopping a simulation} \par
To start the simulation of the current reaction scheme, select 
{\b Start}.  You may also set up the 
simulation engine to run several simulations sequentially (see the section on simulation queues). 
When the simulation starts, the Simulation Engine status window will open.\par
\par
You may manually terminate a simulation by clicking 
{\b [Interrupt Simulation]} on the simulation status 
window.  This will cause the simulation to stop the next time the reaction's state is recorded on disk.  
If you wish to stop the simulation immediately, select {\b Simulation|Abort}.  If not interrupted, the 
simulation will stop when the reaction probabilities are zero, or when either the time or the number 
of events exceeds the limits specified at the "Simulation Settings" window.\par
\par
You may resume a simulation which has been manually interrupted by clicking {\b [Interrupt 
Simulation]}.  To do so, select {\b Simulation|Resume}.  Reaction simulations terminated by 
{\b Simulation|Abort}.\par
\par
{\b Setting up a simulation queue} \par
Once one simulation has begun, you can queue up to eight additional reaction schemes for 
subsequent simulation.  This lets you, for example, prepare several simulations and run them 
overnight.  You queue a reaction simulation by selecting {\b Simulation|Start} , as you would for any 
other simulation.  CKS tells you that the reaction has been automatically placed at the end of the 
queue.\par
\par
You may not alter a reaction scheme that has been placed in the simulation queue unless you first 
remove it from the queue.  If you wish to view the queue or make changes to it (i.e. alter the order 
or cancel a simulation), select {\b Simulation|View Queue}. Additional help is available at that window.\par
\par
\par
{\b For more information:} \par
\pard \fi720\sl0
{\uldb Setting Simulation Options}{\v SIMULATION_SETTINGS} \par
{\uldb Working with a Simulation Queue}{\v QUEUE}\par
{\uldb The Active Simulation}{\v SIMULATION_STATUSWIN} \par
\pard \sl0 
\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}SIMULATION_SETTINGS}
${\footnote {\fs16\up6 $}Setting Simulation Options}
K{\footnote {\fs16\up6 K}Simulation Options;simulation settings;general settings;number of events;number of molecules;particles;random number;}
+{\footnote {\fs16\up6 +}Help:065}
\plain \fs22 \b Setting Simulation Options\plain \par
\par
\par
\plain \fs22 These parameters are necessary to operate the simulator.  The settings are in three groups:  the 
General Settings and Limits, which must be specified for all simulations, and the settings for the 
Equilibrium Detect option, which can be used if the reaction scheme has reversible steps.\par
\par
{\b General settings} \par
TOTAL NUMBER OF MOLECULES specifies the initial number of 
{\ul particles}{\v DEFINITION_PARTICLE}  in the reaction 
simulation.  They are apportioned among species having non-zero initial concentration.  The number 
should be large enough to span the dynamic range of initial concentrations expected in the 
simulation.  Larger numbers will reduce stochastic noise in the simulated data, but also extend the 
computer time required to reach a given point in the simulation.  The largest number allowed is 
2,147,483,647, the minimum is 1.  \par
\par
RECORD STATE AT INTERVALS OF:  xxx EVENTS.  Although the state of the system is 
accurately maintained at all times in memory, it is only saved to disk at fixed intervals.  This number 
gives the interval length.  The smallest number is 1, saving after every 
{\ul event}{\v DEFINITION_EVENT} , and the largest is 
4,294,967,295.  \par
\par
RANDOM NUMBER SEED is an integer between 1 and 30,000 used for initializing the 
random number string which propagates the simulation.\par
\par
{\b Simulation limits} \par
TOTAL NUMBER OF EVENTS is the maximum number of events which can occur in a given 
simulation.  When this maximum is reached the simulation will end.  From 1 to 4,294,967,295 events 
can be specified. \par
\par
STOP WHEN SIMULATION TIME EXCEEDS:  xxx TIME UNITS is an optional setting to cause the 
simulation to be automatically stopped when a particular time is reached in the reaction, even if the 
maximum number of events has not been exceeded.  It is entered in the time units selected when 
the reaction file was created. Floating point or scientific notation formats may be used, with 
exponents in the range -308 to 308.  Enter a value of 0 (zero) to disable the option.  \par
\par
{\b Equilibrium detect} \par
This sets up an option for detecting and emulating equilibria during the course of a simulation.  Use 
of this option can result in significant savings in computer time. Select the topic line a the bottom 
of this page for detailed information on this. \par
\par
\par
The following pushbuttons are available at the bottom of the dialog window.  \par
\par
{\b [OK]} accepts all values in the window and closes it.  \par
\par
{\b [Defaults]} resets all data entry fields and radio buttons to their default values. \par
\par
{\b [Undo]} restores all data to their values when the window was first opened.\par
\par
\par
{\b Other relevant topics:} \par
\pard \fi720\sl0
{\uldb Equilibrium Detect}{\v EQUILIBRIUM_DETECT} \par
{\uldb The Active Simulation}{\v SIMULATION_STATUSWIN} \par
\pard \sl0 
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}QUEUE}
${\footnote {\fs16\up6 $}Working with a Simulation Queue}
K{\footnote {\fs16\up6 K}queue;simulation;multiple simulations}
\plain \fs22 \b Working with a Simulation Queue\plain \par
\plain \fs22 \par
The simulation queue allows you to run more than one simulation without having to be there to start 
it. You place a simulation in the queue by selecting {\b Simulation|Start}.  At the View Simulation 
Queue window, you may change the queue order and cancel simulations by removing reactions 
from the queue.\par
\par
The queue listbox displays all the reaction schemes waiting for simulation in the order they will be 
run. Select a reaction file name by clicking on it. {\b [Remove This]} cancels the simulation by 
removing it from the queue.  {\b [To Top]} places this reaction at the top of the queue, making it the 
next reaction to be simulated.\par
\par
{\b [Remove All]} removes all reactions from the queue.\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}SIMULATION_STATUSWIN}
${\footnote {\fs16\up6 $}Simulation Status Window}
K{\footnote {\fs16\up6 K}simulation;status;running a simulation;interrupting a simulation;multiple simulations}
\plain \fs22 \b The Active Simulation\plain  \par
\par
\par
\plain \fs22 When a simulation is started, the Simulation Engine status window opens. It lists the current time in 
the simulated system and the number of elapsed events.  It is updated every time the simulation 
data are saved to disk.  The {\b [Interrupt Simulation]} pushbutton allows you to manually interrupt the 
simulation, view the results, and resume it later, as long as the reaction file has not been modified.\par
\par
While the simulation is running, the CKS main window is available for data entry and plotting.  
Although you cannot access the reaction scheme you are currently simulating, the other eight file 
{\ul slots}{\v DEFINITION_SLOT}  can be used without restriction. Although you may not start a second simulation before the first 
has ended, you may place additional simulations in a queue.\par
\par
When the simulation has ended, a message giving the termination conditions (e.g. probabilities zero, 
or time limit exceeded) will be displayed, along with the total amount of computer time used.  Click 
on the {\b [OK]} pushbutton to return immediately to the main window. The status window will disappear 
automatically after 10 seconds.\par
\par
\par
{\b For more information:} \par
\pard \fi720\sl0
{\uldb Working with a Simulation Queue}{\v QUEUE} \par
\pard \sl0 
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}EQUILIBRIUM_DETECT}
${\footnote {\fs16\up6 $}Equilibrium Detect}
K{\footnote {\fs16\up6 K}equilibrium detect;equilibrium;reversible}
\plain \fs22 \b Equilibrium Detect\plain  \par
\par
\par
\plain \fs22 The equilibrium detect option is intended for systems with one or more reversible reaction steps, any 
of which may come into equilibrium during a simulation.  {\i Reactions which are reversible but are 
written as two forward steps will not be examined for equilibrium} even though they may come into 
equilibrium during a reaction.\par
\par
This option can be selected during programmed temperature simulations, but is inactive because of 
computational requirements. If a temperature profile is used, equilibrium detect will become active 
once the simulation has converted to a constant temperature simulation at the end of the profile.\par
\par
{\b About the option} \par
The core CKS  algorithm is inefficient in simulating equilibria because it spends its time maintaining 
the equilibrium rather than advancing the chemistry.  This option enables special algorithms to be 
used to handle equilibria in a more efficient way.  The simulation does not assume the existence of 
equilibrium.  Rather, CKS monitors the identity of selected 
{\ul events}{\v DEFINITION_EVENT} , and at specific intervals, 
examines the list for how frequently reversible steps are being selected.  If one or more pairs of 
steps is judged to be in equilibrium, an emulation procedure is invoked to advance the chemistry. 
The system is then returned to normal simulation mode and a new equilibrium detect cycle is 
initiated.  This saves substantial computer time without a loss of accuracy.  \par
\par
{\b Using equilibrium detect} \par
Select the "Enabled" radio button if you wish to use this option.  It can be left on even if no 
equilibrium occurs or if no steps are reversible in the reaction scheme,  the simulation will only be 
slowed down a little by the detect cycle.  To explicitly avoid equilibrium detection, select "Disabled".\par
\par
When equilibrium detect is enabled, the data entry fields for the option will be come active.  \par
\par
EQUIL. TEST CYCLE LENGTH sets the number of events included in a detect cycle. The optimum 
length for the cycle will depend on the reaction scheme, i.e.  number of reversible steps, relative 
rates of reversible and non-reversible steps, and so on.  Typically, values between 100 and 500 are 
good starting points.  \par
\par
SELECTION FREQUENCY is used to diagnose whether a particular reversible reaction is in 
equilibrium.  Equilibrium is found if one or more reversible pairs is selected to occur at least 
(selection frequency) % of the total number of events in the current test cycle, and the forward and 
reverse steps of each pair are selected with frequencies at least (selection frequency) % of each 
other.  Typically values of 80-90% provide sufficient accuracy.  \par
\par
\par
{\b Other relevant topics:} \par
\par
\pard \fi720\sl0
{\uldb Setting up a Linear Temperature Program}{\v TEMPERATURE_LINEAR}\par
{\uldb Programmed Temperature - Select External Profile}{\v TEMPERATURE_EXTPROF_EDIT} \par
\pard \sl0 
\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}MENU_RESULTS}
${\footnote {\fs16\up6 $}Using the Results Menu}
K{\footnote {\fs16\up6 K}Results Menu;Displaying Results;Plotting Results}
+{\footnote {\fs16\up6 +}Help:040}
\plain \fs22  \b Using the Results Menu\plain  \par
\par
\par
\plain \fs22 Select {\b Plot Results...} to plot the results of a simulation.  A window opens to let you select the type 
of plot.  This menu is available only after a simulation of the current reaction scheme has been 
performed.  You may also view the results of a simulation that was run previously and saved, unless 
any changes to the reaction file have been made since then.  External data in the form of a text file 
can be imported and displayed as well.\par
\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}PLOT_SELECT}
${\footnote {\fs16\up6 $}Selecting Plots of Simulation Results}
K{\footnote {\fs16\up6 K}Simulation Results;Viewing Simulation Results;plot types;external data;select species;data points;plotting results;selecting plot;overlaying data;}
+{\footnote {\fs16\up6 +}Help:060}
\plain \fs22 \b Selecting Plots of Simulation Results\plain  \par
\par
\par
\plain \fs22 You may choose which portions of the simulation data to plot, and also select an external data file to 
overlay onto the simulation results.  To plot data, follow these steps:\par
\par
{\b\ 1. Select the plot type} \par
\sect \sectd \sbknone\marglsxn1626 

Click on any of the active checkboxes at the top of the window.  The abbreviations "Conc" and 
"Temp" stand for concentration and temperature, respectively.  The types of plots available 
depend on the reaction conditions originally chosen for the simulation by selecting 
{\b Simulation|Reaction Conditions...}. The concentration versus time (Conc / time) plots are always 
available.  Up to four plot types can be selected at a time.   \par
\sect \sectd \sbknone 

\par
{\b 2. Option: select external data to plot} \par
\sect \sectd \sbknone\marglsxn1626 

Use the {\b [Select file...]} pushbutton if you wish to load an external data file into memory.  The data 
may be, for example, experimental results to compare to the calculated curves, or selected results  
from a previous simulation.  The data must be in the correct format.  Once data are loaded, the 
"External Data:" checkbox is active and the name of the imported file is shown.  Click on it to 
include the external data set in the appropriate plot.  \par
\sect \sectd \sbknone 

\par
{\b 3. Select species to plot} \par
\sect \sectd \sbknone\marglsxn1626 

If you select a Conc/time or Conc/temp plot, then you must also select which reaction species you 
wish to plot.  Use the "Select Species" listbox to select up to seven species to display in any one 
plot.  Select or deselect a species by clicking on it.\par
\sect \sectd \sbknone 

\par
{\b 4. Select the number of data points} \par
\sect \sectd \sbknone\marglsxn1626 

The initially displayed maximum is the total number of data points or 1000, whichever is smaller.  
You may override the maximum number by clicking on the "Max number to plot" data entry field, 
and typing in a new value.  If you have more than 1000 data points, or type in a number less than 
the total available, the points displayed will be evenly spaced to span the full range of the data. \par
\par
\sect \sectd \sbknone 

\par
The pushbuttons at the bottom of the window allow you to draw a plot or close the plot session.  \par
\par
{\b [Close]} returns you to the CKS main window.\par
\par
{\b [Plot]} draws the plot(s).  A new window will be opened to display them.  \par
\par
\plain \fs22 \par
{\b For more information:} \par
\pard \fi720\sl0
{\uldb External Data Format}{\v EXTERNAL_DATA} \par
\pard \sl0 
\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}EXTERNAL_DATA}
${\footnote {\fs16\up6 $}External Data Format}
K{\footnote {\fs16\up6 K}external data;external data format;programmed temperature profile;}
\plain \fs22 \b External Data Format\plain  \fs22 \par
\par
\par
{\b File format} \par
The data must be in text format.  The first line optionally may contain two words to identify the data types to 
the plotting routines.  These words can be in any mixture of upper/lower case.  The first word must be 
either TIME or TEMPERATURE; it can be preceded by an asterisk (*).  The second word must be 
CONCENTRATION, VOLUME, PRESSURE (or TEMPERATURE if the first word was TIME).  If this line specifying 
data types is absent, then the user will be prompted for the correct data type when the plot is constructed. 
\par 
\par
The remaining lines in the text files should each contain two entries in floating point or scientific notation 
format (exponents may range from -308 to 308), giving the values of the external data, separated by one or more blanks.  The first 
value in each line will be read as time or temperature, and the second value will be read as 
concentration, volume, pressure or temperature.  Any line which does not have two valid numeric 
values is skipped in the input procedure.  \par
\par
{\b Examples} \par
\par
1. The general format looks like:\par
\par
\f5 \pard \fi180
\b\fs22
time concentration \par
0.0     1.0e-1\par
1.3     0.6e-1\par
1.1e1   0.4e-1\par
2.5e1   0.0\par
\par \pard \plain
\par
2. Annotating a file\par
\par
If the file you wish to plot is a 
{\ul programmed temperature profile}{\v DEFINITION_TEMP_PROFILE}, put an asterisk (*) at the beginning 
of the first line, so that it reads\par
\par
\f5 \pard \fi180
\b\fs22
*time\tab temperature\par
\par \pard \plain
\par
This lets you use the same file for setting your reaction conditions and for overlaying onto simulation 
results.\par
\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}PLOTWIN}
${\footnote {\fs16\up6 $}Plotting Your Data}
K{\footnote {\fs16\up6 K}plot;plot window}
\plain \fs22 \b Plotting Your Data\plain  \par
\par
\par
\plain \fs22 The plot you selected for your simulation data is displayed at this window.  You may use the 
following pushbuttons to change the appearance of your plot, save the plot to a file, and generate a 
draft hardcopy of your plot.\par
\par
{\b [Close]} returns you to the Simulation Results window.\par
\par
{\b [Axes...]} allows you to change the limits of your plot and choose your tick mark interval.\par
\par
{\b [Attributes...]} lets you customize the appearance of your plot.\par
\par
{\b [Save...]} allows you to save the results displayed in the plot to a file in graphical or text format.\par
\par
{\b [Print...]} lets you send the plot directly to an attached printer.\par
\par
\par
{\b For more information:} \par
\pard \fi720\sl0
{\uldb Adjusting Plot Limits}{\v PLOTWIN_AXES} \par
{\uldb Plot Attributes}{\v PLOTWIN_ATTRIBUTES} \par
{\uldb Saving the Current Plot as a File}{\v PLOTWIN_SAVE} \par
{\uldb Printing the Plot}{\v PLOTWIN_PRINT} \par
\pard \sl0 
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}PLOTWIN_AXES}
${\footnote {\fs16\up6 $}Adjusting Plot Limits}
K{\footnote {\fs16\up6 K}Plot Limits;plot axes}
+{\footnote {\fs16\up6 +}Help:080}
\plain \fs22 \b Adjusting Plot Limits\plain  \par
\par
\par
\plain \fs22 You can modify the horizontal and vertical limits of the plot, the number of tic marks, and the 
number of decimal places for the axis labels.\par
\par
The minimum and maximum limits can be set to any desired range. You may use any tic mark 
interval, with a limit of 40 tics on an axis. Up to 5 decimal places can be specified. To change any of 
these values, click on the data entry field for the value to be changed and type in the new value 
using floating point or scientific notation formats, or integers as appropriate.\par
\par
\par
The following pushbuttons are available:\par
\par
{\b [OK]} accepts the current values, closes this window and redraws the plot using the new limits.  \par
\par
{\b [Undo]} resets the limits to their values when the dialog panel was activated.  \par
\par
{\b [Defaults]} resets the limits to their default values.  The default values are set by the minimum and 
maximum values of the data sets being displayed, allowing all available data to be visible in the 
plots.  \par
\par
{\b [Previous]} sets the limits to those used for the most recent plot of the data set.  \par
\par
\par \pard
\page 

\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}PLOTWIN_SAVE}
${\footnote {\fs16\up6 $}Saving the Current Plot as a File}
K{\footnote {\fs16\up6 K}Saving a Plot;HPGL Output;PostScript Output;Tabular Output;simulation results;output;encapsulated PostScript Output;}
+{\footnote {\fs16\up6 +}Help:090}
\plain \fs22 \b Saving the Current Plot as a File\plain \fs22 \par
\par
\par
{\b File Formats} \par
The plot displayed on the screen can be saved to a disk file in the following formats:\par
\par
o  as a standard PostScript file\par
o  as an encapsulated PostScript file for import into other documents\par
o  as an HPGL (Hewlett-Packard Graphics Language) file \par
o  as a text file containing plot data in tabular form which can be imported into other software for 
plotting or data analysis.  \par
\par
If the file is saved in graphical format it will have attributes (linestyles, colors, plot limits, etc.) 
equivalent to those used to create the current plot(s) in the plot window.  If the file is saved in text 
format, it will contain the simulation data visible in the current plot window.  \par
\par
{\b Orientation} \par
You may select between landscape (horizontal) and portrait (vertical) formats for your plot.  This 
rotates the plot by 90 degrees and rescales the x- and y-axes accordingly.\par
\par
{\b Color} \par
SAVE AS MONOCHROME allows you to create a graphics file in black and white, rather than with 
the colors displayed.  This option allows you to accomodate a variety of presentation needs and 
printer capabilities.  If this option remains unchecked, the plot will be saved with the colors that 
appear on your screen.\par
\par
{\b To save your plot to a file:} \par
1.  Select the file format.\par
2.  For plot files, select the orientation, and if you choose, the monochrome option.\par
3.  Click {\b [Create File...]}.  This opens a filename selection window.\par
4.  Specify a name and directory for the file to be created.\par
5.  Click {\b [OK]}  in the filename dialogue box.\par
\par
\par
The following pushbuttons are available:\par
\par
{\b [Close]} closes this window without creating a new output file.\par
\par
{\b [Create File...]} opens a filename selection window where you specify the name and location of the
plot file.  A new file is created when you select {\b [OK]} at this window.\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}PLOTWIN_PRINT}
${\footnote {\fs16\up6 $}Printing the Plot}
K{\footnote {\fs16\up6 K}print;printing the plot;hardcopy;}
\plain \fs22 \b Printing the Plot\plain \fs22 \par
\par
\par
You may print a plot of the results of your simulation directly on a printer connected to your 
computer.  This lets you generate hardcopies rapidly, but possibly at lower resolution than saving a 
plot to a file.  CKS displays information on your default printer and printer driver, and allows you 
to select available printer options.\par
\par
{\b Print as Monochrome} \par
Checking this box causes your plot to be sent to the printer with all color information removed. The plot 
will be printed in black and white, even if your printer has the capability for color printing. 
This option allows you to accomodate a variety of presentation needs and printer 
qualities.  If this option remains unchecked, the plot is sent to your printer with color information 
that produces a color print using the current selected screen color set.
\par
\par
\par
The following pushbuttons are available:\par
\par
{\b [Close]} returns you to the plot window without printing a plot.\par
\par
{\b [Start Print]} prints the plot according to the selected options.\par
\par
{\b [Cancel Print]} cancels a print job. It is only available when the print job is active.\par
\par
{\b [Printer Setup]} opens the printer setup dialog window for your operating system.\par
\par \pard
\page 



\pard \sl0 
#{\footnote {\fs16\up6 #}SUBJECTS}
${\footnote {\fs16\up6 $}Help subject index}
K{\footnote {\fs16\up6 K}Topics}
\plain \fs22 \b Help Subject Index\plain  \fs22 \par
\par
\par
{\uldb The Active Simulation}{\v SIMULATION_STATUSWIN} \par
{\uldb Adjusting Plot Limits}{\v PLOTWIN_AXES} \par
{\uldb Constant Temperature}{\v TEMPERATURE_CONSTANT} \par 
{\uldb Conventions Used in CKS Help}{\v CONVENTIONS} \par
{\uldb Creating Reaction Files}{\v FILE_CREATE} \par
{\uldb Editing a Rate Law}{\v RATE_LAW_EDIT} \par
{\uldb Entering and Editing Species Data}{\v SPECIES_DATA} \par
{\uldb Equilibrium Detect}{\v EQUILIBRIUM_DETECT} \par
{\uldb External Data Format}{\v EXTERNAL_DATA} \par
{\uldb File selection windows}{\v FILE_SELECTION} \par
{\uldb How to Run a Simulation :  a quick tutorial}{\v TUTORIAL} \par
{\uldb Listboxes}{\v LISTBOXES} \par
{\uldb Overview of CKS}{\v OVERVIEW} \par
{\uldb Plot Attributes}{\v PLOTWIN_ATTRIBUTES} \par
{\uldb Plotting Your Data}{\v PLOTWIN} \par
{\uldb Pressure Options}{\v PRESSURE} \par
{\uldb Printing the Plot}{\v PLOTWIN_PRINT} \par
{\uldb Programmed Temperature - Select External Profile}{\v TEMPERATURE_EXTPROF_EDIT} \par
{\uldb Rate Constants}{\v RATE_CONSTANTS} \par
{\uldb Rate Law}{\v RATE_LAW} \par
{\uldb Reaction Conditions}{\v REACTION_CONDITIONS} \par
{\uldb The Reaction Scheme}{\v REACTION_DATA_ENTRY} \par
{\uldb The Reaction Step}{\v REACTION_STEP} \par
{\uldb Saving the Current Plot as a File}{\v PLOTWIN_SAVE} \par
{\uldb Selecting Plots of Simulation Results}{\v PLOT_SELECT} \par
{\uldb Selecting Units for a New Reaction Scheme}{\v UNITS} \par
{\uldb Setting Application Options}{\v FILE_PREFERENCES} \par
{\uldb Setting Simulation Options}{\v SIMULATION_SETTINGS} \par
{\uldb Setting Species Concentrations}{\v VERIFY_SPECCONC} \par
{\uldb Setting up a Linear Temperature Program}{\v TEMPERATURE_LINEAR} \par
{\uldb Temperature Options}{\v TEMPERATURE} \par
{\uldb Using the Edit Menu}{\v MENU_EDIT} \par
{\uldb Using the File Menu}{\v MENU_FILE} \par
{\uldb Using the Main Menus}{\v MAIN_MENU} \par
{\uldb Using the Main Window}{\v MAIN_WINDOW} \par
{\uldb Using the Notebook}{\v NOTEBOOK} \par
{\uldb Using the Results Menu}{\v MENU_RESULTS} \par
{\uldb Using the Simulation Menu}{\v MENU_SIMULATION} \par
{\uldb Using the View Menu}{\v MENU_VIEW} \par
{\uldb Variable Temperature}{\v TEMPERATURE_VARIABLE} \par
{\uldb Verifying Species Data}{\v VERIFY_SPECDATA} \par
{\uldb Volume options}{\v VOLUME} \par
{\uldb Working with a Simulation Queue}{\v QUEUE} \par
\par \pard\page


\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_ASCII}
\plain \fs22 ASCII format\par
\par
This format is the American Standard Code for Information Interchange. The computer uses this code 
to convert standard symbols such as punctuation, numerals, upper and lower case letters and certain 
control characters (line feed, for example) to the form used internally.\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_CHECKBOX}
\plain \fs22 checkbox\par
\par
One or more checkboxes are provided for some program options to allow  settings to be selected. 
None or all may be chosen in any combination.\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_CLICK}
\plain \fs22 \plain \fs22 click\par
\par
A single-click of the left mouse button.\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_CLIPBOARD}
\plain \fs22 clipboard\par
\par
This is a location where reaction steps cut or copied from the reaction scheme are placed.\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_DATA_ENTRY_FIELD}
\plain \fs22 data entry field\par
\par
Dialog windows for data input have one or more spaces where numbers or text can be typed. These 
data entry fields become active when the cursor is placed on them.\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_DETERMINISTIC}
\plain \fs22 deterministic\par
\par
A deterministic simulation is one in which a system of equations is solved to predict the time history of 
a reacting system.\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_DOUBLE_CLICK}
\plain \fs22 \plain \fs22 double-click\par
\par
Two rapid clicks of the left mouse button.\par
\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_DRAG_AND_DROP}
\plain \fs22 \plain \fs22 drag-and-drop\par
\par
Select an icon (by clicking on it with the left mouse button), and move it (by holding the right mouse 
button down and moving the pointer to the desired location).\par
\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_EVENT}
\plain \fs22 event\par
\par
A simulation is carried out by selecting reaction steps from the reaction scheme, and updating the 
system. Each selection cycle is an event.\par
\par \pard\page




\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_HELP_LINE}
\plain \fs22 \plain \fs22 help line\par
\par
Describes the function of the main window item your mouse is currently pointing to.\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_INDUCTIVE}
\plain \fs22 inductive\par
\par
This is a method of reasoning which is commonly used to develop complex models. Experimental data 
are analyzed to extract a simple mechanism, which is then used to make specific predictions about the 
behavior of the system under different conditions. These predictions are compared to new experiments, 
which are used in turn to refine the model in an iterative way.\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_LISTBOX}
\plain \fs22 listbox\par
\par
A set of names or lines of data are displayed in a listbox so that one or more can be selected for 
actions such as data entry. There are three types of listboxes: \par
o  single selection, where only one item can be selected at a time,\par
o  multiple selection, where more than one item can be selected, and\par
o  drop down, which shows only the currently selected item but is displayed in full when its button is 
pushed.\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_MULTITASKING}
\plain \fs22 multitasking\par
\par
A multitasking operating system is one which allows the computer to work on several programs at once. 
A computer program can also be designed to be internally multitasking, carrying out several tasks at 
once. In this way, computer time is used very efficiently.\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_PARTICLE}
\plain \fs22 particle\par
\par
A simulation system contains a number of particles used to represent molecules, atoms and 
pseudo-species which participate in the reaction scheme. Each particle is proportional to a 
concentration or an amount, depending on the reaction conditions selected.\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_PATH}
\plain \fs22 path\par
\par
A path is the sequence of directory names leading from the root directory on a disk to a particular file. 
Its form is drive:folder:subfolder:filename.\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_PSEUDO_SPECIES}
\plain \fs22 pseudo-species\par
\par
Simulations can be structured so that parts of molecules, or particular groups of molecules are followed 
in the mechanism, rather than actual molecules. These pseudo-species are useful devices for 
simplifying reaction schemes, or highlighting important features of a reaction.\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_PULL_DOWN_MENU}
\plain \fs22 pull-down menu\par
\par
Selection of one of the menu names listed in the main window causes a list of options to appear 
beneath it. This list is a pull-down menu.\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_PUSHBUTTON}
\plain \fs22 pushbutton\par
\par
Pushbuttons located on dialog windows allow various actions to be chosen.\par
\par \pard\page

\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_RADIO_BUTTON}
\plain \fs22 radio button\par
\par
A set of radio buttons is used to represent several possible settings available for a particular program 
option. They are used when one, but only one, of the settings must be selected.\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_RANDOM_NUMBER_SEED}
\plain \fs22 random number seed\par
\par
This is a number between 1 and 30000 which is used to initiate a sequence of random numbers for 
selection of events in the simulation.\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_REACTION_LISTBOX}
\plain \fs22 \plain \fs22 reaction listbox\par
\par
The reaction steps of the currently active reaction scheme are displayed in the reaction listbox.\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_SLOT}
\plain \fs22 slot\par
\par
Up to nine reaction schemes can be kept active in memory at once. Each scheme is placed in a slot, 
the nine slots are shown using \plain \b\fs22 File|Select\plain \fs22 .\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_STOCHASTIC}
\plain \fs22 stochastic\par
\par
The stochastic simulation is a probabilistic method for predicting the time evolution of a reacting 
system.\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_TEMP_CONV_STAND}
\plain \fs22 temperature convergence standard\par
\par
This is a parameter used in variable temperature calculations. When the temperature is updated, it is 
calculated iteratively from the enthalpy and temperature-dependent heat capacity of the system. The 
convergence standard is used to compare temperatures from two successive iterations. If their 
difference is less than the standard, the calculation has converged.\par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_TEMP_PROFILE}
\plain \fs22 temperature profile\par
\par
This is a list of time-temperature points which establishes the instantaneous temperature in a
simulation. \par
\par \pard\page



\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_TIME_STEP}
\plain \fs22 time step\par
\par
This is the calculated time which elapses between two events in a simulation.\par
\par \pard\page

\pard \sl0
#{\footnote {\fs16\up6 #}DEFINITION_TIMEBASE}
\plain \fs22 timebase\par
\par
The timebase in a simulation is the time history of the events which are selected.
\par \pard\page



}
